Substitution Models For Download?

Question

[dani.boobyer]

Hi,

I need to add some substitution models into PAML (e.g. BLOSUM62, RtREV, VT). Is there anywhere I can download these from, ideally in .dat format?

Thanks for your help. Dani.

Answer 1

[aravind ramesh]

Hai Dani,

1) For PAM250 2 For BLOSUM62 3) For Rt REV Matrices 4) For VT Matrices 5) A very good article regarding substitutional Matrices

Hope this helps

Answer 2

[Woa]

There was an issue with BLOSUM 62. Be sure you get the 'correct' BLOSUM series of substitution tables

Answer 3

[bilouorama]

You can try this web site : http://www.genome.jp/aaindex/ You'll find about 90 substitution matrices with the publication related. It's an old resource but still full of many references.